PDBsum entry 3d2d

Oxidoreductase

PDB id: 3d2d

Contents

Protein chain

500 a.a. *

Ligands

NAG-NAG-MAN-MAN-MAN-MAN

NAG

FAD

REN

Waters ×18

* Residue conservation analysis

PDB id:

3d2d

Name:

Oxidoreductase

Title:

Structure of berberine bridge enzyme in complex with (s)-reticuline

Structure:

Berberine bridge-forming enzyme. Chain: a. Synonym: bbe. Tetrahydroprotoberberine synthase. Reticuline oxidase. Engineered: yes

Source:

Eschscholzia californica. California poppy. Organism_taxid: 3467. Gene: bbe1. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

2.80Å R-factor: 0.191 R-free: 0.241

Authors:

A.Winkler,A.Lyskowski,P.Macheroux,K.Gruber

Key ref:

A.Winkler et al. (2008). A concerted mechanism for berberine bridge enzyme. Nat Chem Biol, 4, 739-741. PubMed id: 18953357 DOI: 10.1038/nchembio.123

Date:

08-May-08 Release date: 28-Oct-08

Protein chain

P30986  (RETO_ESCCA) -  Reticuline oxidase from Eschscholzia californica

Seq: 538 a.a.

Struc: 500 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.21.3.3 - reticuline oxidase.
• Pathway: Stylopine biosynthesis
• Reaction: (S)-reticuline + O2 = (S)-scoulerine + H2O2 + H⁺

(S)-reticuline (Bound ligand (Het Group name = REN) corresponds exactly) + O2 = (S)-scoulerine + H2O2 + H(+)

• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nchembio.123

Nat Chem Biol 4:739-741 (2008)

PubMed id: 18953357

A concerted mechanism for berberine bridge enzyme.

A.Winkler, A.Lyskowski, S.Riedl, M.Puhl, T.M.Kutchan, P.Macheroux, K.Gruber.

ABSTRACT

Berberine bridge enzyme catalyzes the conversion of (S)-reticuline to (S)-scoulerine by formation of a carbon-carbon bond between the N-methyl group and the phenolic ring. We elucidated the structure of berberine bridge enzyme from Eschscholzia californica and determined the kinetic rates for three active site protein variants. Here we propose a catalytic mechanism combining base-catalyzed proton abstraction with concerted carbon-carbon coupling accompanied by hydride transfer from the N-methyl group to the N5 atom of the FAD cofactor.

Selected figure(s)

Figure 1.
(a) Overall reaction catalyzed by BBE^1 (Enzyme Commission number 1.21.3.3). (b) Schematic representation of the protein structure. The N-terminal FAD-binding subdomains are shown in blue and green (including the C-terminal -helical stretch in light green), and the central substrate binding domain is shown in magenta. N-linked sugar residues (blue) and the FAD cofactor (orange) are represented as stick models. The amino acids involved in the bicovalent linkage of FAD are shown in green. (c) Active site environments of the structures from the monoclinic crystals showing polar amino acids as dark green stick models. Alternate conformations were observed for Glu417. The flavin cofactor is shown in orange with its dual mode of attachment to the protein backbone via His104 and Cys166 represented in green. (d) Interactions between the substrate and active site amino acids (green). The substrate is shown in yellow, and FAD is shown in orange. Distances are indicated in Å.

The above figure is reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2008, 4, 739-741) copyright 2008.